In this example, the second microarray is just a mirror image of the first for test purposes as I couldn't find two similarly size examples. The reflection means that the registration is probably not as good as you'd expect from a true comparison, but it serves its purpose to highlight the possibilities and downsides of the technique.

The technique could be much improved with good examples and a clearer statement of requirements.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

One problem is that the graphs have been produced using anti-aliasing. A process that trades accuracy for aesthetic appearance. Which means that if you try to subtract one image from another you get a big blurry streak of color: cluster1 - cluster8

With some more processing it should be possible to retrieve a single, contiguous line from those fat, fuzzy, discontinuous streaks. Albiet that it might take several passes to do so.

But the show stopper as far as achieving your single similarity figure is the lack of any indication of how to rate the two posted images for similarity.

It is obvious that if the two lines, once reduced to continuous, single pixel wide lines, exactly overlaid each other, that would constitute 100% similarity. But how do you rate divergence?

Possibilities:

You might consider any two pixels that do not exactly align a percentage point of divergence.